tbuckley/cabot-search huggingface dataset:
A shift from travel-associated cases to autochthonous transmission with Berlin as epicentre of the monkeypox outbreak in Germany, May to June 2022
Authors: Regina Selb, Dirk Werber, Gerhard Falkenhorst, Gyde Steffen, Raskit Lachmann, Claudia Ruscher, Sarah McFarland, Alexander Bartel, Lukas Hemmers, Uwe Koppe, Klaus Stark, Viviane Bremer, Klaus Jansen
Journal: Eurosurveillance (2022)

By 22 June 2022, 521 cases of monkeypox were notified in Germany. The median age was 38 years (IQR: 32–44); all cases were men. In Berlin, where 69% of all cases occurred, almost all were men who have sex with men. Monkeypox virus likely circulated unrecognised in Berlin before early May. Since mid-May, we observed a shift from travel-associated infections to mainly autochthonous transmission that predominantly took place in Berlin, often in association with visits to clubs and parties.
Niraparib plus nivolumab or niraparib plus ipilimumab in patients with platinum-sensitive advanced pancreatic cancer: a randomised, phase 1b/2 trial
Authors: Kim A Reiss, Rosemarie Mick, Ursina Teitelbaum, Mark O'Hara, Charles Schneider, Ryan Massa, Thomas Karasic, Rashmi Tondon, Chioma Onyiah, Mary Kate Gosselin, Alyssa Donze, Susan M Domchek, Robert H Vonderheide
Journal: The Lancet Oncology (2022)
Blood pressure measurement using only a smartphone
Authors: Lorenz Frey, Carlo Menon, Mohamed Elgendi
Journal: npj Digital Medicine (2022)

Abstract Hypertension is an immense challenge in public health. As one of the most prevalent medical conditions worldwide, it is a major cause of premature death. At present, the detection, diagnosis and monitoring of hypertension are subject to several limitations. In this review, we conducted a literature search on blood pressure measurement using only a smartphone, which has the potential to overcome current limitations and thus pave the way for long-term ambulatory blood pressure monitoring on a large scale. Among the 333 articles identified, we included 25 relevant articles over the past decade (November 2011–November 2021) and analyzed the described approaches to the types of underlying data recorded with smartphone sensors, the signal processing techniques applied to construct the desired signals, the features extracted from the constructed signals, and the algorithms used to estimate blood pressure. In addition, we analyzed the validation of the proposed methods against reference blood pressure measurements. We further examined and compared the effectiveness of the proposed approaches. Among the 25 articles, 23 propose an approach that requires direct contact between the sensor and the subject and two articles propose a contactless approach based on facial videos. The sample sizes in the identified articles range from three to 3000 subjects, where 8 articles used sample sizes of 85 or more subjects. Furthermore, 10 articles include hypertensive subjects in their participant pools. The methodologies applied for the evaluation of blood pressure measurement accuracy vary considerably among the analyzed articles. There is no consistency regarding the methods for blood pressure data collection and the reference blood pressure measurement and validation. Moreover, no established protocol is currently available for the validation of blood pressure measuring technologies using only a smartphone. We conclude the review with a discussion of the results and with recommendations for future research on the topic.
“Rapid reinfections with different or same Omicron SARS-CoV-2 sub-variants”
Authors: Ihm Vera-Lise, Ensle Dominik, Reiter Elisabeth, Huber Kerstin, Förster Raffael, Xaver Angelika, Aßheuer Tibor, Barna Jusztina, Karnthaler Ursula, Haidvogel Jochen, Kirsch David, Jordan John-Hendrik
Journal: Journal of Infection (2022)
More than one way to skin a cat: Addressing the arbitration problem in developmental science
Authors: Denis Tatone
Journal: Behavioral and Brain Sciences (2022)

Abstract David Pietraszewski's theory of social groups offers a developmentally plausible account of how we reason about group membership, as it delineates clear boundaries to the hypothesis space that children must navigate. Merits notwithstanding, the account remains silent with respect to the arbitration problem: It does not explain how children can appropriately select among competing frames when interpreting social interactions.
Triadic conflict “primitives” can be reduced to welfare trade-off ratios
Authors: Wenhao Qi, Edward Vul, Adena Schachner, Lindsey J. Powell
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski proposes four triadic “primitives” for representing social groups. We argue that, despite surface differences, these triads can all be reduced to similar underlying welfare trade-off ratios, which are a better candidate for social group primitives. Welfare trade-off ratios also have limitations, however, and we suggest there are multiple computational strategies by which people recognize and reason about social groups.
Emerging technologies revolutionise insect ecology and monitoring
Authors: Roel van Klink, Tom August, Yves Bas, Paul Bodesheim, Aletta Bonn, Frode Fossøy, Toke T. Høye, Eelke Jongejans, Myles H.M. Menz, Andreia Miraldo, Tomas Roslin, Helen E. Roy, Ireneusz Ruczyński, Dmitry Schigel, Livia Schäffler, Julie K. Sheard, Cecilie Svenningsen, Georg F. Tschan, Jana Wäldchen, Vera M.A. Zizka, Jens Åström, Diana E. Bowler
Journal: Trends in Ecology & Evolution (2022)

Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.
Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature
Authors: Abigail Wong-Rolle, Qiang Dong, Yunhua Zhu, Prajan Divakar, Jyh Liang Hor, Noemi Kedei, Madeline Wong, Desiree Tillo, Elizabeth A Conner, Arun Rajan, David S Schrump, Chengcheng Jin, Ronald N Germain, Chen Zhao
Journal: Journal for ImmunoTherapy of Cancer (2022)

Background The lung intratumor microbiome influences lung cancer tumorigenesis and treatment responses, but detailed data on the extent, location, and effects of microbes within lung tumors are missing, information needed for improved prognosis and treatment. Methods To address this gap, we developed a novel spatial meta-transcriptomic method simultaneously detecting the expression level of 1,811 host genes and 3 microbe targets (bacteria, fungi, and cytomegalovirus). After rigorous validation, we analyzed the spatial meta-transcriptomic profiles of tumor cells, T cells, macrophages, other immune cells, and stroma in surgically resected tumor samples from 12 patients with early-stage lung cancer. Results Bacterial burden was significantly higher in tumor cells compared with T cells, macrophages, other immune cells, and stroma. This burden increased from tumor-adjacent normal lung and tertiary lymphoid structures to tumor cells to the airways, suggesting that lung intratumor bacteria derive from the latter route of entry. Expression of oncogenic β-catenin was strongly correlated with bacterial burden, as were tumor histological subtypes and environmental factors. Conclusions Intratumor bacteria were enriched with tumor cells and associated with multiple oncogenic pathways, supporting a rationale for reducing the local intratumor microbiome in lung cancer for patient benefit. Trial registration number NCT00242723 , NCT02146170 .
Tackling racism: moving beyond rhetoric to turn theory into practice
Authors: James Nazroo
Journal: BMJ (2022)

<h3>Background</h3> Current evidence connects impulse control disorders (ICDs) to dopaminergic replacement therapy used for the treatment of Parkinson9s disease (PD). Common ICDs include hypersexuality, pathological gambling, compulsive shopping and binge eating. The underlying neuropathology is thought to be due to sensitisation of the dopaminergic system in the striatum and related neurocircuitry. <h3>Aim</h3> To investigate the effect of rewarding visual cues on dopamine neurotransmission in PD patients with ICDs. <h3>Methods</h3> Ten ICD PD patients and five PD controls underwent two randomised positron emission tomography (PET) scans with 11C-raclopride (RAC) after a medication challenge with levodopa while observing neutral or rewarding (gambling, sex, food and money) images. Scans were analysed using region-of-interest approach. <h3>Results</h3> The ICD PD group showed a significant decrease of RAC binding in ventral striatum (p=0.001) and caudate nucleus (p=0.015) in response to rewarding images (compared to neutral images), where in PD controls there was no difference. <h3>Discussion</h3> Our PET results suggest a significant increase in the release of endogenous dopamine in ventral striatum and caudate nucleus in PD patients with ICDs and further support the role of dopaminergic pathways in mediating ICDs. The response to visual stimuli alone may be of relevance to new treatment strategies.
Longer-term benefit of luspatercept in transfusion-dependent lower-risk myelodysplastic syndromes with ring sideroblasts
Authors: Amer M. Zeidan, Uwe Platzbecker, Guillermo Garcia-Manero, Mikkael A. Sekeres, Pierre Fenaux, Amy E. DeZern, Peter L. Greenberg, Michael R. Savona, Joseph G. Jurcic, Amit K. Verma, Ghulam J. Mufti, Rena Buckstein, Valeria Santini, Jeevan K. Shetty, Rodrigo Ito, Jennie Zhang, George Zhang, Xianwei Ha, Jay T. Backstrom, Rami S. Komrokji
Journal: Blood (2022)

Luspatercept is an approved therapy for selected patients with lower risk myelodysplasia requiring transfusion despite erythropoiesis-stimulating agents, based on the early results of a randomized trial against placebo. Zeidan and colleagues report that after a median of 26 months follow-up, 27% of patients commencing luspatercept were continuing therapy. Their updated analyses confirm that a significant minority (45%) of eligible patients can achieve transfusion independence, with a median durability of 30 weeks. These longer follow-up data better quantify the incremental benefit of luspatercept over placebo.
Optimizing treatment approaches for patients with cutaneous melanoma by integrating clinical and pathologic features with the 31-gene expression profile test
Authors: Abel Jarell, Brian R. Gastman, Larry D. Dillon, Eddy C. Hsueh, Sebastian Podlipnik, Kyle R. Covington, Robert W. Cook, Christine N. Bailey, Ann P. Quick, Brian J. Martin, Sarah J. Kurley, Matthew S. Goldberg, Susana Puig
Journal: Journal of the American Academy of Dermatology (2022)
Private versus public: A dual model for resource-constrained conflict representations
Authors: Simon DeDeo
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski's representation scheme is parsimonious and intuitive. However, internal mental representations may be subject to resource constraints that prefer more unusual systems such as sparse coding or compressed sensing. Pietraszewski's scheme may be most useful for understanding how agents communicate. Conflict may be driven in part by the complex interplay between parsimonious public representations and more resource-efficient internal ones.
<scp>HLA</scp>‐matched related donor hematopoietic stem cell transplantation is a suitable treatment in adolescents and adults with sickle cell disease: Comparison of myeloablative and non‐myeloablative approaches
Authors: Nathalie Dhedin, Florian Chevillon, Martin Castelle, Virginie Lavoipière, Loic Vasseur, Jean‐Hugues Dalle, Laure Joseph, Florence Beckerich, Nimrod Buchbinder, Tereza Coman, Frédéric Garban, Alina Ferster, Stephanie Nguyen, Nicolas Boissel, Jean‐Benoit Arlet, Corinne Pondarre
Journal: American Journal of Hematology (2022)

Appendix Supporting Information Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Compassion within conflict: Toward a computational theory of social groups informed by maternal brain physiology
Authors: S. Shaun Ho, Richard N. Rosenthal, Helen Fox, David Garry, Meroona Gopang, Mikaela J. Rollins, Sarah Soliman, James E. Swain
Journal: Behavioral and Brain Sciences (2022)

Abstract Benevolent intersubjectivity developed in parent–infant interactions and compassion toward friend and foe alike are non-violent interventions to group behavior in conflict. Based on a dyadic active inference framework rooted in specific parental brain mechanisms, we suggest that interventions promoting compassion and intersubjectivity can reduce stress, and that compassionate mediation may resolve conflicts.
Using laboratory intergroup conflict and riots as a “stress test”
Authors: James M. Allen, Daniel C. Richardson
Journal: Behavioral and Brain Sciences (2022)

Abstract We apply the author's computational approach to groups to our empirical work studying and modelling riots. We suggest that assigning roles in particular gives insight, and measuring the frequency of bystander behaviour provides a method to understand the dynamic nature of intergroup conflict, allowing social identity to be incorporated into models of riots.
Editorial Cycles and Continuity of <i>Diabetes Care</i>
Authors: Matthew C. Riddle, George Bakris, Lawrence Blonde, Andrew J.M. Boulton, Jessica Castle, Linda DiMeglio, Linda Gonder-Frederick, Frank Hu, Steven Kahn, Sanjay Kaul, Robert Moses, Stephen Rich, Julio Rosenstock, Elizabeth Selvin, Adrian Vella, Judith Wylie-Rosett
Journal: Diabetes Care (2022)
More “us,” less “them”: An appeal for pluralism – and stand-alone computational theorizing – in our science of social groups
Authors: David Pietraszewski
Journal: Behavioral and Brain Sciences (2022)

Abstract The target article is an appeal to allow explicit computational theorizing into the study of social groups. Some commentators took this proposal and ran with it, some had questions about it, and some were confused or even put off by it. But even the latter did not seem to outright disagree – they thought the proposal was mutually exclusive with some other enterprise, when in fact it is not. Unfortunately, scientists studying social groups have not yet avoided the thread-bare trope of the blind men studying the different parts of the elephant: We see mutual exclusivity when we should see complementarity. I hope we can all take the next steps of examining how the different enterprises and approaches within our area of research might all fit together into a unified whole.
Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes
Authors: Mitchell J Syberg-Olsen, Arkadiy I Garber, Patrick J Keeling, John P McCutcheon, Filip Husnik
Journal: Molecular Biology and Evolution (2022)

Abstract Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes.
Factors Associated with Severe Outcomes Among Immunocompromised Adults Hospitalized for COVID-19 — COVID-NET, 10 States, March 2020–February 2022
Authors: Jason Robert C. Singson, Pam Daily Kirley, Huong Pham, Gretchen Rothrock, Isaac Armistead, James Meek, Evan J. Anderson, Libby Reeg, Ruth Lynfield, Susan Ropp, Alison Muse, Christina B. Felsen, Melissa Sutton, H. Keipp Talbot, Fiona P. Havers, Christopher A. Taylor, Arthur Reingold, Shua J. Chai, Nisha B. Alden, Kim Yousey-Hindes, Kyle P. Openo, Erica Bye, Mark A. Montoya, Grant Barney, Kevin Popham, Nasreen Abdullah, William Schaffner
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Vaccinated patients were defined as those with a positive SARS-CoV-2 test result from a specimen collected ≥14 days after either the second dose of a 2-dose vaccination series or after 1 dose of a single-dose vaccine.When not otherwise specified, vaccinated patients include those who might have received additional or booster doses.Vaccinated patients without additional or booster doses include both those eligible and those not yet eligible for an additional or booster dose.Vaccinated patients with additional booster doses received additional or booster doses on or after August 13, 2021, with a positive SARS-CoV-2 test result from a specimen collected ≥14 days after receipt of additional or booster doses.† https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/prevention.html§ https://www.cdc.gov/coronavirus/2019-ncov/vaccines/recommendations/immuno.html¶ https://www.cdc.gov/coronavirus/2019-ncov/need-extra-precautions/peoplewith-medical-conditions.html;https://www.covid19treatmentguidelines.nih.gov/overview/prioritization-of-therapeutics/ ** California, Colorado, Connecticut, Georgia, Michigan, Minnesota, New Mexico, New York, Oregon, and Tennessee.Data from four other states in COVID-NET were not available for this analysis.† † Excluded admissions for labor/obstetrics, trauma, psychiatric conditions, or inpatient surgery.§ § Standardized COVID-NET medical chart abstraction identified the following immunocompromising conditions: AIDS or CD4+ count <200, complement deficiency, graft versus host disease, HIV infection, immunoglobulin deficiency/immunodeficiency, immunosuppressive therapy (within 12 months before admission), leukemia, Hodgkin or non-Hodgkin lymphoma, metastatic cancer, multiple myeloma, solid organ malignancy, steroid therapy (within 2 weeks of admission), and transplant history involving hematopoietic stem cells or solid organs.
Using routine emergency department data for syndromic surveillance of acute respiratory illness, Germany, week 10 2017 until week 10 2021
Authors: T. Sonia Boender, Wei Cai, Madlen Schranz, Theresa Kocher, Birte Wagner, Alexander Ullrich, Silke Buda, Rebecca Zöllner, Felix Greiner, Michaela Diercke, Linus Grabenhenrich
Journal: Eurosurveillance (2022)

BackgroundThe COVID-19 pandemic expanded the need for timely information on acute respiratory illness at population level.AimWe explored the potential of routine emergency department data for syndromic surveillance of acute respiratory illness in Germany.MethodsWe used routine attendance data from emergency departments, which continuously transferred data between week 10 2017 and 10 2021, with ICD-10 codes available for > 75% of attendances. Case definitions for acute respiratory infection (ARI), severe acute respiratory infection (SARI), influenza-like illness (ILI), respiratory syncytial virus infection (RSV) and COVID-19 were based on a combination of ICD-10 codes, and/or chief complaints, sometimes combined with information on hospitalisation and age.ResultsWe included 1,372,958 attendances from eight emergency departments. The number of attendances dropped in March 2020 during the first COVID-19 pandemic wave, increased during summer, and declined again during the resurge of COVID-19 cases in autumn and winter of 2020/21. A pattern of seasonality of respiratory infections could be observed. By using different case definitions (i.e. for ARI, SARI, ILI, RSV) both the annual influenza seasons in the years 2017-2020 and the dynamics of the COVID-19 pandemic in 2020/21 were apparent. The absence of the 2020/21 influenza season was visible, parallel to the resurge of COVID-19 cases. SARI among ARI cases peaked in April-May 2020 (17%) and November 2020-January 2021 (14%).ConclusionSyndromic surveillance using routine emergency department data can potentially be used to monitor the trends, timing, duration, magnitude and severity of illness caused by respiratory viruses, including both influenza viruses and SARS-CoV-2.
Understanding the bidirectional interactions between two-dimensional materials, microorganisms, and the immune system
Authors: Guotao Peng, Bengt Fadeel
Journal: Advanced Drug Delivery Reviews (2022)

Two-dimensional (2D) materials such as the graphene-based materials, transition metal dichalcogenides, transition metal carbides and nitrides (MXenes), black phosphorus, hexagonal boron nitride, and others have attracted considerable attention due to their unique physicochemical properties. This is true not least in the field of medicine. Understanding the interactions between 2D materials and the immune system is therefore of paramount importance. Furthermore, emerging evidence suggests that 2D materials may interact with microorganisms - pathogens as well as commensal bacteria that dwell in and on our body. We discuss the interplay between 2D materials, the immune system, and the microbial world in order to bring a systems perspective to bear on the biological interactions of 2D materials. The use of 2D materials as vectors for drug delivery and as immune adjuvants in tumor vaccines, and 2D materials to counteract inflammation and promote tissue regeneration, are explored. The bio-corona formation on and biodegradation of 2D materials, and the reciprocal interactions between 2D materials and microorganisms, are also highlighted. Finally, we consider the future challenges pertaining to the biomedical applications of various classes of 2D materials.
Coalitionary psychology and group dynamics on social media
Authors: Jeff Deminchuk, Sandeep Mishra
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski's model allows understanding group dynamics through the lens of evolved coalitionary psychology. This framework is particularly relevant to understanding group dynamics on social media platforms, where coalitions based on salience of group identity are prominent and generate unique frictions. We offer testable hypotheses derived from the model that may help to shed light on social media behavior.
Shadow banning, astroturfing, catfishing, and other online conflicts where beliefs about group membership diverge
Authors: Jordan W Suchow
Journal: Behavioral and Brain Sciences (2022)

Abstract Drawing from conflicts observed in online communities (e.g., astroturfing and shadow banning), I extend Pietraszewski's theory to accommodate phenomena dependent on the intersubjectivity of groups, where representations of group membership (or beliefs about group membership) diverge. Doing so requires enriching representations to include other agents and their beliefs in a process of recursive mentalizing.